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- PDB-8dti: Cryo-EM structure of Arabidopsis SPY in complex with GDP-fucose -

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Basic information

Entry
Database: PDB / ID: 8dti
TitleCryo-EM structure of Arabidopsis SPY in complex with GDP-fucose
ComponentsProbable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
KeywordsTRANSFERASE / O-fucosyltransferase / SPY
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase activity / negative regulation of gibberellic acid mediated signaling pathway / peptide-O-fucosyltransferase / protein O-linked glycosylation via fucose / peptide-O-fucosyltransferase activity / gibberellic acid mediated signaling pathway / cytokinin-activated signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / flower development ...protein N-acetylglucosaminyltransferase activity / negative regulation of gibberellic acid mediated signaling pathway / peptide-O-fucosyltransferase / protein O-linked glycosylation via fucose / peptide-O-fucosyltransferase activity / gibberellic acid mediated signaling pathway / cytokinin-activated signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / flower development / regulation of reactive oxygen species metabolic process / rhythmic process / cell differentiation / nucleus / cytoplasm
Similarity search - Function
: / Sel1-like repeat / Sel1-like repeats. / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. ...: / Sel1-like repeat / Sel1-like repeats. / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKumar, S. / Zhou, Y. / Dillard, L. / Borgnia, M.J. / Bartesaghi, A. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of the full length Arabidopsis SPY with complete TPRs
Authors: Kumar, S. / Zhou, Y.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
B: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,7364
Polymers210,5582
Non-polymers1,1792
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY / SPY / GDP-fucose protein O-fucosyltransferase SPINDLY


Mass: 105278.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SPY, At3g11540, F24K9.29 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96301, protein O-GlcNAc transferase, peptide-O-fucosyltransferase
#2: Chemical ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SPY in complex with GDP-fucose / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 52.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
2Latitudeimage acquisition
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182947 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039687
ELECTRON MICROSCOPYf_angle_d0.50113262
ELECTRON MICROSCOPYf_dihedral_angle_d7.5011399
ELECTRON MICROSCOPYf_chiral_restr0.0381521
ELECTRON MICROSCOPYf_plane_restr0.0031702

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